ngsReports::FastQC

/fast/users/a1647910/20190122_Q96K97_NoStress_RNASeq/2_alignedData/FastQC

Setup

FastQC Summary

Summary statistics for all libraries

Filename	Total	Flagged As Poor Quality	Sequence Length	%GC
Q1Aligned.sortedByCoord.out.bam	80,528,674	0	8-150	43
Q2Aligned.sortedByCoord.out.bam	92,097,647	0	8-150	43
Q4Aligned.sortedByCoord.out.bam	103,912,111	0	8-150	43
Q5Aligned.sortedByCoord.out.bam	86,862,161	0	3-150	44
W1Aligned.sortedByCoord.out.bam	92,264,849	0	8-150	43
W2Aligned.sortedByCoord.out.bam	87,720,625	0	8-150	44
W3Aligned.sortedByCoord.out.bam	90,411,804	0	8-150	43
W4Aligned.sortedByCoord.out.bam	105,852,840	0	7-150	43
W5Aligned.sortedByCoord.out.bam	82,170,056	0	8-150	43

Read Totals

Library Sizes ranged between 80,528,674 and 105,852,840 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Hsapiens Genome

GC Content Distributions for all reads showing theoretical GC content from the Hsapiens Genome

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented Summary

Total overrepresented sequences for each library

Overrepresented Sequences

## Overrepresented_sequences missing from Q1Aligned.sortedByCoord.out.bam

## Overrepresented_sequences missing from Q2Aligned.sortedByCoord.out.bam

## Overrepresented_sequences missing from Q4Aligned.sortedByCoord.out.bam

## Overrepresented_sequences missing from Q5Aligned.sortedByCoord.out.bam

## Overrepresented_sequences missing from W1Aligned.sortedByCoord.out.bam

## Overrepresented_sequences missing from W2Aligned.sortedByCoord.out.bam

## Overrepresented_sequences missing from W3Aligned.sortedByCoord.out.bam

## Overrepresented_sequences missing from W4Aligned.sortedByCoord.out.bam

## Overrepresented_sequences missing from W5Aligned.sortedByCoord.out.bam

## No overrepresented sequences were detected by FastQC

Adapter Content

Universal Adapter Content

Kmer Content

## Kmer_Content missing from Q1Aligned.sortedByCoord.out.bam

## Kmer_Content missing from Q2Aligned.sortedByCoord.out.bam

## Kmer_Content missing from Q4Aligned.sortedByCoord.out.bam

## Kmer_Content missing from Q5Aligned.sortedByCoord.out.bam

## Kmer_Content missing from W1Aligned.sortedByCoord.out.bam

## Kmer_Content missing from W2Aligned.sortedByCoord.out.bam

## Kmer_Content missing from W3Aligned.sortedByCoord.out.bam

## Kmer_Content missing from W4Aligned.sortedByCoord.out.bam

## Kmer_Content missing from W5Aligned.sortedByCoord.out.bam

## No Kmers were detected by FastQC